my clutch only stays about 3 inchs off the floor in which all of it is clutch should it be all the way up?
It should be all the way up. Check and make sure the rod that goes into the back of the master cylinder is properly adjusted. And realize that the pedal on the LEFT feeds into the plunger on the RIGHT of the master cylinder when you're crawling around under the dash.
There should be two springs under the dash--one for the brake, one for the clutch, to return the pedals to the full upright position. Seems like I had to replace one with a junk yard donor. It was either that, or I had to replace the one at the clutch slave. Either way, there's two springs, and two rods that get adjusted for the clutch.
Sounds like you may need to take the same approach I did--just start replacing everything connected, one at a time, until it's fixed.
-Brad